SEATTLE  Federal officials have proposed designating nearly all of northwest Washington's inland waters -- about 2,500 square miles -- as critical habitat for killer whales, the first major development since the creatures were listed as endangered last year.

Following a public comment period, the habitat designation could become official by the end of the year, the National Marine Fisheries Service said Friday in a news release. It would mean that within the outlined area, no federal activities can take place unless officials demonstrate that the habitat will not be harmed.

The proposed area encompasses parts of Haro Strait, the waters around the San Juan Islands, the Strait of Juan de Fuca and all of Puget Sound except for Hood Canal, because there is little evidence the orcas swim there. Eighteen military sites covering nearly 112 square miles of habitat are exempt.

"It looks like we're getting the tools in place to provide orcas with the protection that hopefully will get them to the point of recovery," said Patti Goldman, an attorney with the environmental law firm Earthjustice.

But Kathy Fletcher, executive director of People for Puget Sound, and Fred Felleman, of Ocean Advocates, questioned whether the proposed area is enough: Besides military areas, it excludes any waters less than 20 feet deep. They said shorelines are crucial to the health of the ecosystem overall, and in particular to salmon -- the primary food source of Puget Sound's orcas. Herring, which the salmon eat, live in shallow subtidal zones.

"This is a major gap," Fletcher said. "When something is proposed that might screw up the habitat of Puget Sound" -- a dock for a construction project, for instance -- "it's on the shoreline. The habitat of the salmon is as important as the waters where the orcas actually swim themselves."

Felleman said that overall, he was pleased with the proposal, but that he would like to see the waters off the state's western coast designated as critical habitat as well: That's where the orcas spend at least some of the winter, he said, and it's also where they could be troubled by Navy activities.

Fisheries Service spokesman Brian Gorman invited Fletcher and Felleman to raise such points during the public comment period.

"People are encouraged to point out where they think we need a little more work," he said.

The federal agency's 44-page report on the proposal notes that the designation of critical habitat could lead to revised limits for commercial salmon fishermen and new standards for sewer and stormwater discharge.

The "southern resident" population of orcas in Puget Sound -- believed to have numbered 140 or more in the last century -- has suffered several major periods of decline since the 1960s, when the whales were caught for aquariums. The population rebounded to 97 in the 1990s, then declined to 79 in 2001. Currently, there are 90 whales, with several calves recently born.

Pollution and a decline in prey are believed to be their biggest threats, though stress from whale-watch boats and underwater sonar tests by the Navy are also concerns.

The National Marine Fisheries Service initially refused to list the whales under the Endangered Species Act, finding that they were not distinct from other orcas around the world -- a finding based on a classification of the species written in 1758. In 2002, eight environmental groups sued, and U.S. District Judge Robert Lasnik ordered the agency to reconsider, using updated science.

The fisheries service eventually agreed that the Puget Sound orcas needed protection, leading to the listing in November. Farm and property rights groups have challenged the listing in federal court in Seattle, saying it could lead to "needless water and land-use restrictions on Washington farms, especially those located near rivers inhabited by salmon," the orcas' prime food source.

The fisheries service also said it expects to release its draft orca recovery plan for public comment within the next month.